Variant 2-121530839-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001395891.1(CLASP1):c.196-514A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0449 in 666,100 control chromosomes in the GnomAD database, including 899 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.037 ( 154 hom., cov: 33)

Exomes 𝑓: 0.047 ( 745 hom. )

Consequence

CLASP1
NM_001395891.1 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0260

Variant links:

Genes affected

CLASP1 (HGNC:17088): (cytoplasmic linker associated protein 1) CLASPs, such as CLASP1, are nonmotor microtubule-associated proteins that interact with CLIPs (e.g., CLIP170; MIM 179838). CLASP1 is involved in the regulation of microtubule dynamics at the kinetochore and throughout the spindle (Maiato et al., 2003 [PubMed 12837247]).[supplied by OMIM, Mar 2008]

CLASP1 links:

CLASP1-AS1 (HGNC:55328): (CLASP1 antisense RNA 1)

CLASP1-AS1 links:

RNU4ATAC (HGNC:34016): (RNA, U4atac small nuclear) The small nuclear RNA (snRNA) encoded by this gene is part of the U12-dependent minor spliceosome complex. In addition to the encoded RNA, this ribonucleoprotein complex consists of U11, U12, U5, and U6atac snRNAs. The U12-dependent spliceosome acts on approximately 700 specific introns in the human genome. Defects in this gene are a cause of microcephalic osteodysplastic primordial dwarfism type 1 (MOPD). [provided by RefSeq, Jul 2011]

RNU4ATAC links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 2-121530839-T-C is Benign according to our data. Variant chr2-121530839-T-C is described in ClinVar as [Benign]. Clinvar id is 1242503.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLASP1	NM_001395891.1 link	c.196-514A>G		intron_variant		ENST00000696935.1	NP_001382820.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLASP1	ENST00000696935.1 link	c.196-514A>G		intron_variant			NM_001395891.1	ENSP00000512981.1		A0A8V8TLP7

Frequencies

GnomAD3 genomes

AF:

0.0370

AC:

5635

AN:

152108

Hom.:

153

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0148

Gnomad AMI

AF:

0.0526

Gnomad AMR

AF:

0.0376

Gnomad ASJ

AF:

0.0628

Gnomad EAS

AF:

0.139

Gnomad SAS

AF:

0.0542

Gnomad FIN

AF:

0.0248

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0421

Gnomad OTH

AF:

0.0296

GnomAD3 exomes

AF:

0.0511

AC:

6238

AN:

121986

Hom.:

200

AF XY:

0.0504

AC XY:

3362

AN XY:

66758

show subpopulations

Gnomad AFR exome

AF:

0.0127

Gnomad AMR exome

AF:

0.0525

Gnomad ASJ exome

AF:

0.0590

Gnomad EAS exome

AF:

0.132

Gnomad SAS exome

AF:

0.0456

Gnomad FIN exome

AF:

0.0272

Gnomad NFE exome

AF:

0.0423

Gnomad OTH exome

AF:

0.0479

GnomAD4 exome

AF:

0.0473

AC:

24298

AN:

513874

Hom.:

745

Cov.:

AF XY:

0.0472

AC XY:

12962

AN XY:

274568

show subpopulations

Gnomad4 AFR exome

AF:

0.0154

Gnomad4 AMR exome

AF:

0.0510

Gnomad4 ASJ exome

AF:

0.0565

Gnomad4 EAS exome

AF:

0.115

Gnomad4 SAS exome

AF:

0.0474

Gnomad4 FIN exome

AF:

0.0287

Gnomad4 NFE exome

AF:

0.0429

Gnomad4 OTH exome

AF:

0.0460

GnomAD4 genome

AF:

0.0370

AC:

5638

AN:

152226

Hom.:

154

Cov.:

AF XY:

0.0362

AC XY:

2695

AN XY:

74422

show subpopulations

Gnomad4 AFR

AF:

0.0149

Gnomad4 AMR

AF:

0.0377

Gnomad4 ASJ

AF:

0.0628

Gnomad4 EAS

AF:

0.139

Gnomad4 SAS

AF:

0.0539

Gnomad4 FIN

AF:

0.0248

Gnomad4 NFE

AF:

0.0421

Gnomad4 OTH

AF:

0.0293

Alfa

AF:

0.0395

Hom.:

Bravo

AF:

0.0386

Asia WGS

AF:

0.0660

AC:

232

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 10, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

6.4

DANN

Benign

0.70

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over